Merge pull request #3602 from mnoergaard/update_petsurfer

ENH: Update PETsurfer interface

Author: effigies

nipype/interfaces/freesurfer/model.py

@@ -420,6 +420,14 @@ class GLMFitInputSpec(FSTraitedSpec):
         argstr="--logan %s %s %f",
         desc="RefTac TimeSec tstar   : perform Logan kinetic modeling",
     )
+    bp_clip_neg = traits.Bool(
+        argstr="--bp-clip-neg",
+        desc="set negative BP voxels to zero",
+    )
+    bp_clip_max = traits.Float(
+        argstr="--bp-clip-max %f",
+        desc="set BP voxels above max to max",
+    )
     force_perm = traits.Bool(
         argstr="--perm-force",
         desc="force perumtation test, even when design matrix is not orthog",

nipype/interfaces/freesurfer/petsurfer.py

@@ -458,10 +458,25 @@ class GTMPVCOutputSpec(TraitedSpec):
     yhat_with_noise = File(
         desc="4D PET file with full FOV of signal estimate (yhat) with noise after PVC (smoothed with PSF)",
     )
+    eres = File(
+        desc="4D PET file of residual error after PVC (smoothed with PSF)",
+    )
+    tissue_fraction = File(
+        desc="4D PET file of tissue fraction before PVC",
+    )
+    tissue_fraction_psf = File(
+        desc="4D PET file of tissue fraction after PVC (smoothed with PSF)",
+    )
+    seg = File(
+        desc="Segmentation file of regions used for PVC",
+    )
+    seg_ctab = File(
+        desc="Color table file for segmentation file",
+    )
 
 
 class GTMPVC(FSCommand):
-    """create an anatomical segmentation for the geometric transfer matrix (GTM).
+    """Perform Partial Volume Correction (PVC) to PET Data.
 
     Examples
     --------
@@ -536,6 +551,15 @@ def _list_outputs(self):
         outputs["gtm_stats"] = os.path.join(pvcdir, "gtm.stats.dat")
         outputs["reg_pet2anat"] = os.path.join(pvcdir, "aux", "bbpet2anat.lta")
         outputs["reg_anat2pet"] = os.path.join(pvcdir, "aux", "anat2bbpet.lta")
+        outputs["eres"] = os.path.join(pvcdir, "eres.nii.gz")
+        outputs["tissue_fraction"] = os.path.join(
+            pvcdir, "aux", "tissue.fraction.nii.gz"
+        )
+        outputs["tissue_fraction_psf"] = os.path.join(
+            pvcdir, "aux", "tissue.fraction.psf.nii.gz"
+        )
+        outputs["seg"] = os.path.join(pvcdir, "aux", "seg.nii.gz")
+        outputs["seg_ctab"] = os.path.join(pvcdir, "aux", "seg.ctab")
 
         # Assign the conditional outputs
         if self.inputs.save_input:
@@ -562,7 +586,7 @@ def _list_outputs(self):
         return outputs
 
 
-class MRTMInputSpec(GLMFitInputSpec):
+class MRTM1InputSpec(GLMFitInputSpec):
     mrtm1 = traits.Tuple(
         File(exists=True),
         File(exists=True),
@@ -572,20 +596,20 @@ class MRTMInputSpec(GLMFitInputSpec):
     )
 
 
-class MRTM(GLMFit):
+class MRTM1(GLMFit):
     """Perform MRTM1 kinetic modeling.
 
     Examples
     --------
-    >>> mrtm = MRTM()
+    >>> mrtm = MRTM1()
     >>> mrtm.inputs.in_file = 'tac.nii'
     >>> mrtm.inputs.mrtm1 = ('ref_tac.dat', 'timing.dat')
     >>> mrtm.inputs.glm_dir = 'mrtm'
     >>> mrtm.cmdline
     'mri_glmfit --glmdir mrtm --y tac.nii --mrtm1 ref_tac.dat timing.dat'
     """
 
-    input_spec = MRTMInputSpec
+    input_spec = MRTM1InputSpec
 
 
 class MRTM2InputSpec(GLMFitInputSpec):
@@ -614,7 +638,7 @@ class MRTM2(GLMFit):
     input_spec = MRTM2InputSpec
 
 
-class LoganRefInputSpec(GLMFitInputSpec):
+class LoganInputSpec(GLMFitInputSpec):
     logan = traits.Tuple(
         File(exists=True),
         File(exists=True),
@@ -625,16 +649,16 @@ class LoganRefInputSpec(GLMFitInputSpec):
     )
 
 
-class LoganRef(GLMFit):
-    """Perform Logan reference kinetic modeling.
+class Logan(GLMFit):
+    """Perform Logan kinetic modeling.
     Examples
     --------
-    >>> logan = LoganRef()
+    >>> logan = Logan()
     >>> logan.inputs.in_file = 'tac.nii'
     >>> logan.inputs.logan = ('ref_tac.dat', 'timing.dat', 2600)
     >>> logan.inputs.glm_dir = 'logan'
     >>> logan.cmdline
     'mri_glmfit --glmdir logan --y tac.nii --logan ref_tac.dat timing.dat 2600'
     """
 
-    input_spec = LoganRefInputSpec
+    input_spec = LoganInputSpec

nipype/interfaces/freesurfer/tests/test_auto_GLMFit.py

@@ -13,6 +13,12 @@ def test_GLMFit_inputs():
         args=dict(
             argstr="%s",
         ),
+        bp_clip_max=dict(
+            argstr="--bp-clip-max %f",
+        ),
+        bp_clip_neg=dict(
+            argstr="--bp-clip-neg",
+        ),
         calc_AR1=dict(
             argstr="--tar1",
         ),

nipype/interfaces/freesurfer/tests/test_auto_GTMPVC.py

@@ -207,6 +207,9 @@ def test_GTMPVC_inputs():
 
 def test_GTMPVC_outputs():
     output_map = dict(
+        eres=dict(
+            extensions=None,
+        ),
         gtm_file=dict(
             extensions=None,
         ),
@@ -256,6 +259,18 @@ def test_GTMPVC_outputs():
         reg_rbvpet2anat=dict(
             extensions=None,
         ),
+        seg=dict(
+            extensions=None,
+        ),
+        seg_ctab=dict(
+            extensions=None,
+        ),
+        tissue_fraction=dict(
+            extensions=None,
+        ),
+        tissue_fraction_psf=dict(
+            extensions=None,
+        ),
         yhat=dict(
             extensions=None,
         ),

nipype/interfaces/freesurfer/tests/test_auto_LoganRef.py nipype/interfaces/freesurfer/tests/test_auto_Logan.py

@@ -1,8 +1,8 @@
 # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
-from ..petsurfer import LoganRef
+from ..petsurfer import Logan
 
 
-def test_LoganRef_inputs():
+def test_Logan_inputs():
     input_map = dict(
         allow_ill_cond=dict(
             argstr="--illcond",
@@ -13,6 +13,12 @@ def test_LoganRef_inputs():
         args=dict(
             argstr="%s",
         ),
+        bp_clip_max=dict(
+            argstr="--bp-clip-max %f",
+        ),
+        bp_clip_neg=dict(
+            argstr="--bp-clip-neg",
+        ),
         calc_AR1=dict(
             argstr="--tar1",
         ),
@@ -214,14 +220,14 @@ def test_LoganRef_inputs():
             xor=("weight_file", "weight_inv", "weight_sqrt"),
         ),
     )
-    inputs = LoganRef.input_spec()
+    inputs = Logan.input_spec()
 
     for key, metadata in list(input_map.items()):
         for metakey, value in list(metadata.items()):
             assert getattr(inputs.traits()[key], metakey) == value
 
 
-def test_LoganRef_outputs():
+def test_Logan_outputs():
     output_map = dict(
         beta_file=dict(
             extensions=None,
@@ -271,7 +277,7 @@ def test_LoganRef_outputs():
             extensions=None,
         ),
     )
-    outputs = LoganRef.output_spec()
+    outputs = Logan.output_spec()
 
     for key, metadata in list(output_map.items()):
         for metakey, value in list(metadata.items()):

nipype/interfaces/freesurfer/tests/test_auto_MRTM.py nipype/interfaces/freesurfer/tests/test_auto_MRTM1.py

@@ -1,8 +1,8 @@
 # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
-from ..petsurfer import MRTM
+from ..petsurfer import MRTM1
 
 
-def test_MRTM_inputs():
+def test_MRTM1_inputs():
     input_map = dict(
         allow_ill_cond=dict(
             argstr="--illcond",
@@ -13,6 +13,12 @@ def test_MRTM_inputs():
         args=dict(
             argstr="%s",
         ),
+        bp_clip_max=dict(
+            argstr="--bp-clip-max %f",
+        ),
+        bp_clip_neg=dict(
+            argstr="--bp-clip-neg",
+        ),
         calc_AR1=dict(
             argstr="--tar1",
         ),
@@ -214,14 +220,14 @@ def test_MRTM_inputs():
             xor=("weight_file", "weight_inv", "weight_sqrt"),
         ),
     )
-    inputs = MRTM.input_spec()
+    inputs = MRTM1.input_spec()
 
     for key, metadata in list(input_map.items()):
         for metakey, value in list(metadata.items()):
             assert getattr(inputs.traits()[key], metakey) == value
 
 
-def test_MRTM_outputs():
+def test_MRTM1_outputs():
     output_map = dict(
         beta_file=dict(
             extensions=None,
@@ -271,7 +277,7 @@ def test_MRTM_outputs():
             extensions=None,
         ),
     )
-    outputs = MRTM.output_spec()
+    outputs = MRTM1.output_spec()
 
     for key, metadata in list(output_map.items()):
         for metakey, value in list(metadata.items()):

nipype/interfaces/freesurfer/tests/test_auto_MRTM2.py

@@ -13,6 +13,12 @@ def test_MRTM2_inputs():
         args=dict(
             argstr="%s",
         ),
+        bp_clip_max=dict(
+            argstr="--bp-clip-max %f",
+        ),
+        bp_clip_neg=dict(
+            argstr="--bp-clip-neg",
+        ),
         calc_AR1=dict(
             argstr="--tar1",
         ),

nipype/interfaces/freesurfer/tests/test_auto_OneSampleTTest.py

@@ -13,6 +13,12 @@ def test_OneSampleTTest_inputs():
         args=dict(
             argstr="%s",
         ),
+        bp_clip_max=dict(
+            argstr="--bp-clip-max %f",
+        ),
+        bp_clip_neg=dict(
+            argstr="--bp-clip-neg",
+        ),
         calc_AR1=dict(
             argstr="--tar1",
         ),